Filter Files

There are two parameter files a user can provide if they would like to override or augment the default parameter sets. The first is the “filter file”. It provides acceptable limits for all of the physical properties and functional groups in the default filter. The second is the “newrule file”. If you have a filter you like, but would like to augment it with a set of additional rules, these can be added with a newrule file.

There are four types of statements that can occur in a filter file:

  • physical property limits
  • rules
  • new rules
  • selections

The statements should occur one-per-line in the filter file.

Note

If the appropriate line is not in the filter file, or the value is false, the respective measure will not be used in filtering and its value will not be included in any table-based output.

Physical Property Limits

There are a large number of physical property limits. They occur as three fields on a line. For example:

MIN_HETEROATOMS 2 "Minimum number of heteroatoms"

The first field is the property keyword, the second field is the value assigned to that keyword, and the third field is a brief informational message. There are a fixed number of physical property keywords. No additional physical property keywords can be added by the user. The current keywords and brief definitions of each are listed below.

Hint

The values listed below are those found in the default BlockBuster filter.

Basic Properties

Molecular Weight

Isotopic molecular weight

MIN_MOLWT 130 "Minimum molecular weight"
MAX_MOLWT 781 "Maximum molecular weight"

Heavy Atom Count

Number of non-hydrogen atoms

MIN_NUM_HVY 9 "Minimum number of heavy atoms"
MAX_NUM_HVY 55 "Maximum number of heavy atoms"

Carbon Count

Number of carbons

MIN_CARBONS 3 "Minimum number of carbons"
MAX_CARBONS 41 "Maximum number of carbons"

Hetero-Count

Number of non-carbon and non-hydrogen atoms

MIN_HETEROATOMS 1 "Minimum number of heteroatoms"
MAX_HETEROATOMS 14 "Maximum number of heteroatoms"

Hetero-Atom to Carbon Ratio

Hetero-count/carbon-count

MIN_Het_C_Ratio 0.04 "Minimum heteroatom to carbon ratio"
MAX_Het_C_Ratio 4.0 "Maximum heteroatom to carbon ratio"

Chiral Count

Number of chiral atoms

MIN_CHIRAL_CENTERS 0 "Minimum chiral centers"
MAX_CHIRAL_CENTERS 21 "Maximum chiral centers"

Hydrogen-bond Acceptors

Number of atoms which match any of the following:

  • degree 2, aromatic, non-positive nitrogens
  • electron rich or negative, valence less than 4, non-aromatic nitrogens
  • negatively charged or not electron withdrawn and neutral oxygens
  • degree 1, double bonded, electron rich sulfur
MIN_HBOND_ACCEPTORS 0 "Minimum number of hydrogen-bond acceptors"
MAX_HBOND_ACCEPTORS 13 "Maximum number of hydrogen-bond acceptors"

Hydrogen-bond Donors

Number of hydrogen atoms on nitrogen, oxygen, or sulfur atoms

MIN_HBOND_DONORS 0 "Minimum number of hydrogen-bond donors"
MAX_HBOND_DONORS 9 "Maximum number of hydrogen-bond donors"

Lipinski Acceptors

Number of nitrogens or oxygens

MIN_LIPINSKI_ACCEPTORS 1 "Minimum number of oxygen & nitrogen atoms"
MAX_LIPINSKI_ACCEPTORS 14 "Maximum number of oxygen & nitrogen atoms"

Lipinski Donors

Number of hydrogens attached to nitrogen or oxygen

MIN_LIPINSKI_DONORS 0 "Minimum number of hydrogens on O & N atoms"
MAX_LIPINSKI_DONORS 6 "Maximum number of hydrogens on O & N atoms"

Halide Fraction

Percent of molecular weight from halides

MIN_HALIDE_FRACTION 0.0 "Minimum Halide Fraction"
MAX_HALIDE_FRACTION 0.66 "Maximum Halide Fraction"

Formal Count

Number of atoms with a formal charge (excludes dative)

MIN_COUNT_FORMAL_CRG 0 "Minimum number formal charges"
MAX_COUNT_FORMAL_CRG 4 "Maximum number of formal charges"

Formal Sum

Total formal charge

MIN_SUM_FORMAL_CRG -2 "Minimum sum of formal charges"
MAX_SUM_FORMAL_CRG 2 "Maximum sum of formal charges"

Connected Non-Ring

Considers sets of contiguous (bonded) non-ring atoms

MIN_CON_NON_RING 0 "Minimum number of connected non-ring atoms"
MAX_CON_NON_RING 19 "Maximum number of connected non-ring atoms"

Unbranched Chains

The size of unbranched non-ring chains

MIN_UNBRANCHED 1 "Minimum number of connected unbranched non-ring atoms"
MAX_UNBRANCHED 13 "Maximum number of connected unbranched non-ring atoms"

Total Functional Group Count

Total number of functional groups. Does not count any ring-systems as functional groups. Degree 1 heteroatoms, particularly those with double bonds or dative bonds are considered part of ring systems and do not count as a functional group.

MIN_FCNGRP 0 "Minimum number of functional groups"
MAX_FCNGRP 7 "Maximum number of functional groups"

Note

This is different then the functional group rules.

Ring Systems

Number of ring systems (contiguous systems of ring atoms and bonds)

MIN_RING_SYS 0 "Minimum number of ring systems"
MAX_RING_SYS 5 "Maximum number of ring systems"

Ring Size

Maximum size of any single ring system

MIN_RING_SIZE 0 "Minimum atoms in any ring system"
MAX_RING_SIZE 20 "Maximum atoms in any ring system"

Rotor Count

Number of rotatable bonds. Allows optional adjustment for aliphatic rings following the method of [Oprea-2000].

MIN_ROT_BONDS 0 "Minimum number of rotatable bonds"
MAX_ROT_BONDS 16 "Maximum number of rotatable bonds"
ADJUST_ROT_FOR_RING true "BOOLEAN for whether to estimate degrees of freedom in rings"

Rigid Count

Number of rigid bonds (non-rotatable bonds)

MIN_RIGID_BONDS 4 "Minimum number of rigid bonds"
MAX_RIGID_BONDS 55 "Maximum number of rigid bonds"

LogP

The logP calculation is a derivative of the published XLogP algorithm [Wang-1997]., but reparameterized without the dependence on 3D coordinates or the SYBYL/Mol2 aromaticity model.

XLogP

Calculated LogP

MIN_XLOGP -3.0 "Minimum XLogP"
MAX_XLOGP 6.85 "Maximum XLogP"

Solubility

The solubility predictions are based on using the atom-types from the XLogP algorithm, [Wang-1997], and reparameterizing them based on available solubility data. Rather than a quantitative cutoff, solubility uses categories. The 6 allowable categories are:

  1. insoluble
  2. poorly
  3. moderately
  4. soluble
  5. very
  6. highly

These categories are keywords used in the filter files as follows.

Solubility

Calculated solubility class

MIN_SOLUBILITY insoluble "Minimum solubility"

Pharmacokinetic Predictors

Several secondary filters that are built upon published combinations of simpler properties are available.

Note

All of these properties are used for filtering in the default filters.

Lipinski Violations

Number of allowable Lipinski violations. A single Lipinski violation is considered acceptable. The published work, [Lipinski-1997], allows compounds to pass with a single violation but not multiple violations.

MAX_LIPINSKI 3 "Maximum number of Lipinski violations"

See also

The Lipinski theory section in the Molecular Properties and Predictors chapter.

PSA

Peter Ertl’s, [Ertl-2000], topological polar surface area (phosphorus and sulfur area is optional).

PSA_USE_SandP false "Count S and P as polar atoms"
MIN_2D_PSA 0.0 "Minimum 2-Dimensional (SMILES) Polar Surface Area"
MAX_2D_PSA 205.0 "Maximum 2-Dimensional (SMILES) Polar Surface Area"

See also

The PSA theory section in the Molecular Properties and Predictors chapter.

GSK/Veber

Veber’s measure of bioavailability (PSA > 140 or Rotatable bonds >10). [Veber-2002].

GSK_VEBER false "PSA>140 or >10 rot bonds"

Abbott/Martin

Yvonne Martin’s Abbott Bioavailability Score. This is reported as a probability that F>10% in rats. [Martin-2005]

MIN_ABS 0.11 "Minimum probability F>10% in rats"

Pharmacopia/Egan

Egan egg measure of bioavailability (LogP >5.88 or PSA > 131.6). [Egan-2000]

PHARMACOPIA false "LogP > 5.88 or PSA > 131.6"

Aggregators

Aggregators are small molecules that can interfere with assay results by sequestering protein in an aggregation of small molecules in solution. They appear to have activity in many assays, but in fact are usually not specific inhibitors of the protein in question. Includes two measures of whether a molecule is one of the aggregators defined by Shoichet et. al. [McGovern-2003] [Seidler-2003] The first measure, AGGREGATORS, is whether the molecule is an exact match to one of the approximately 400 published aggregators. The second measure, PRED_AGG, is whether the molecule hits in Shoichet’s QSAR model for predicting aggregators.

Aggregators

Whether a compound is known or predicted to aggregate in concentrations common in virtual screening.

AGGREGATORS true "Eliminate known aggregators"
PRED_AGG false "Eliminate predicted aggregators"

Elemental Filters

The elemental filters are applied in this order:

  1. Test for the existence of any of the metals in the ELIMINATE_METALS filter in the molecule.
  2. Remove salts by stripping away all the disconnected components except for the largest.
  3. Test to make sure only atoms specified in ALLOWED_ELEMENTS filter are in the molecule.

The format of the two elemental filter fields is the keyword followed by a comma delimited list of atomic symbols.

Eliminate Metals

Any molecule with the atoms indicated in ELIMINATE_METALS fail to pass the filter.

ELIMINATE_METALS Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd

Allowed Elements

Molecules with atoms other than those specified by ALLOWED_ELEMENTS fail to pass the filter.

ALLOWED_ELEMENTS H,C,N,O,F,P,S,Cl,Br,I

Functional Group Rules

Rules statements set the limits for the maximum number of the specified type of functional group that may be allowed in the molecule.

The first field of a rule statement is the word RULE in all capital letters. The second field is a number indicating the maximum number of the group allowed in a molecule. The third field is the functional group keyword. Functional-group keywords are case sensitive.

RULE 0 acid_halide

The following is a list of functional groups which filter recognizes by default. Three example matches are provided with the atoms that correspond to each other highlighted. Due to the highly complex nature of the patterns, in particular recursive SMARTS, it is not possible to fully highlight every atom that was included as part of the match.

acetal

_images/acetal-001.png _images/acetal-002.png _images/acetal-003.png

acid_halide

_images/acid_halide-001.png _images/acid_halide-002.png _images/acid_halide-003.png

acyclic_NCN

_images/acyclic_NCN-001.png _images/acyclic_NCN-002.png _images/acyclic_NCN-003.png

acyclic_NS

_images/acyclic_NS-001.png _images/acyclic_NS-002.png _images/acyclic_NS-003.png

acyl_cyanides

_images/acyl_cyanides-001.png _images/acyl_cyanides-002.png _images/acyl_cyanides-003.png

acylhydrazide

_images/acylhydrazide-001.png _images/acylhydrazide-002.png _images/acylhydrazide-003.png

alcohol

_images/alcohol-001.png _images/alcohol-002.png _images/alcohol-003.png

aldehyde

_images/aldehyde-001.png _images/aldehyde-002.png _images/aldehyde-003.png

alkene

_images/alkene-001.png _images/alkene-002.png _images/alkene-003.png

alkylaniline

_images/alkylaniline-001.png _images/alkylaniline-002.png _images/alkylaniline-003.png

alkyl_halide

_images/alkyl_halide-001.png _images/alkyl_halide-002.png _images/alkyl_halide-003.png

alkyl_phosphate

_images/alkyl_phosphate-001.png _images/alkyl_phosphate-002.png _images/alkyl_phosphate-003.png

alkyne

_images/alkyne-001.png _images/alkyne-002.png _images/alkyne-003.png

alphahalo_amine

_images/alphahalo_amine-001.png _images/alphahalo_amine-002.png _images/alphahalo_amine-003.png

alphahalo_ketone

_images/alphahalo_ketone-001.png _images/alphahalo_ketone-002.png _images/alphahalo_ketone-003.png

amide

_images/amide-001.png _images/amide-002.png _images/amide-003.png

aminal

_images/aminal-001.png _images/aminal-002.png _images/aminal-003.png

amine

_images/amine-001.png _images/amine-002.png _images/amine-003.png

amino_acid

_images/amino_acid-001.png _images/amino_acid-002.png _images/amino_acid-003.png

anhydride

_images/anhydride-001.png _images/anhydride-002.png _images/anhydride-003.png

aniline

_images/aniline-001.png _images/aniline-002.png _images/aniline-003.png

arenesulfonyl

_images/arenesulfonyl-001.png _images/arenesulfonyl-002.png _images/arenesulfonyl-003.png

aryl_halide

_images/aryl_halide-001.png _images/aryl_halide-002.png _images/aryl_halide-003.png

azide

_images/azide-001.png _images/azide-002.png _images/azide-003.png

aziridine

_images/aziridine-001.png _images/aziridine-002.png _images/aziridine-003.png

azo

_images/azo-001.png _images/azo-002.png _images/azo-003.png

azocyanamides

_images/azocyanamides-001.png _images/azocyanamides-002.png _images/azocyanamides-003.png

benzyl_ether

_images/benzyl_ether-001.png _images/benzyl_ether-002.png _images/benzyl_ether-003.png

benzyloxycarbonyl_CBZ

_images/benzyloxycarbonyl_CBZ-001.png _images/benzyloxycarbonyl_CBZ-002.png _images/benzyloxycarbonyl_CBZ-003.png

beta_azo_carbonyl

_images/beta_azo_carbonyl-001.png _images/beta_azo_carbonyl-002.png _images/beta_azo_carbonyl-003.png

beta_carbonyl_quat_nitrogen

_images/beta_carbonyl_quat_nitrogen-001.png _images/beta_carbonyl_quat_nitrogen-002.png _images/beta_carbonyl_quat_nitrogen-003.png

beta_halo_carbonyl

_images/beta_halo_carbonyl-001.png _images/beta_halo_carbonyl-002.png _images/beta_halo_carbonyl-003.png

carbamate

_images/carbamate-001.png _images/carbamate-002.png _images/carbamate-003.png

carbamic_acid

_images/carbamic_acid-001.png _images/carbamic_acid-002.png _images/carbamic_acid-003.png

carbodiimide

_images/carbodiimide-001.png _images/carbodiimide-002.png _images/carbodiimide-003.png

carbonate

_images/carbonate-001.png _images/carbonate-002.png _images/carbonate-003.png

carboxylic_acid

_images/carboxylic_acid-001.png _images/carboxylic_acid-002.png _images/carboxylic_acid-003.png

cation_C_Cl_I_P_or_S

_images/cation_C_Cl_I_P_or_S-001.png _images/cation_C_Cl_I_P_or_S-002.png _images/cation_C_Cl_I_P_or_S-003.png

cyanohydrins

_images/cyanohydrins-001.png _images/cyanohydrins-002.png _images/cyanohydrins-003.png

cycloheximide_derivatives

_images/cycloheximide_derivatives-001.png _images/cycloheximide_derivatives-002.png _images/cycloheximide_derivatives-003.png

cyclopropyl

_images/cyclopropyl-001.png _images/cyclopropyl-002.png _images/cyclopropyl-003.png

cytochalasin_derivatives

_images/cytochalasin_derivatives-001.png _images/cytochalasin_derivatives-002.png _images/cytochalasin_derivatives-003.png

dioxane_6MR

_images/dioxane_6MR-001.png _images/dioxane_6MR-002.png _images/dioxane_6MR-003.png

dioxolane_5MR

_images/dioxolane_5MR-001.png _images/dioxolane_5MR-002.png _images/dioxolane_5MR-003.png

di_peptide

_images/di_peptide-001.png _images/di_peptide-002.png _images/di_peptide-003.png

disulfide

_images/disulfide-001.png _images/disulfide-002.png _images/disulfide-003.png

dithioacetal

_images/dithioacetal-001.png _images/dithioacetal-002.png _images/dithioacetal-003.png

dye

_images/dye-001.png _images/dye-002.png _images/dye-003.png

enamine

_images/enamine-001.png _images/enamine-002.png _images/enamine-003.png

enol_ether

_images/enol_ether-001.png _images/enol_ether-002.png _images/enol_ether-003.png

epoxide

_images/epoxide-001.png _images/epoxide-002.png _images/epoxide-003.png

ester

_images/ester-001.png _images/ester-002.png _images/ester-003.png

ether

_images/ether-001.png _images/ether-002.png _images/ether-003.png

fluorenylmethoxycarbonyl_Fmoc

_images/fluorenylmethoxycarbonyl_Fmoc-001.png _images/fluorenylmethoxycarbonyl_Fmoc-002.png _images/fluorenylmethoxycarbonyl_Fmoc-003.png

guanidine

_images/guanidine-001.png _images/guanidine-002.png _images/guanidine-003.png

halide

_images/halide-001.png _images/halide-002.png _images/halide-003.png

halo_alkene

_images/halo_alkene-001.png _images/halo_alkene-002.png _images/halo_alkene-003.png

halopyrimidine

_images/halopyrimidine-001.png _images/halopyrimidine-002.png _images/halopyrimidine-003.png

hemiacetal

_images/hemiacetal-001.png _images/hemiacetal-002.png _images/hemiacetal-003.png

hemiaminal

_images/hemiaminal-001.png _images/hemiaminal-002.png _images/hemiaminal-003.png

hemiketal

_images/hemiketal-001.png _images/hemiketal-002.png _images/hemiketal-003.png

HOBT_esters

_images/HOBT_esters-001.png _images/HOBT_esters-002.png _images/HOBT_esters-003.png

hydrazine

_images/hydrazine-001.png _images/hydrazine-002.png _images/hydrazine-003.png

hydrazone

_images/hydrazone-001.png _images/hydrazone-002.png _images/hydrazone-003.png

hydroxamic_acid

_images/hydroxamic_acid-001.png _images/hydroxamic_acid-002.png _images/hydroxamic_acid-003.png

hydroxylamine

_images/hydroxylamine-001.png _images/hydroxylamine-002.png _images/hydroxylamine-003.png

imine

_images/imine-001.png _images/imine-002.png _images/imine-003.png

iodine

_images/iodine-001.png _images/iodine-002.png _images/iodine-003.png

iodoso

_images/iodoso-001.png _images/iodoso-002.png _images/iodoso-003.png

iodoxy

_images/iodoxy-001.png _images/iodoxy-002.png _images/iodoxy-003.png

isocyanate

_images/isocyanate-001.png _images/isocyanate-002.png _images/isocyanate-003.png

isonitrile

_images/isonitrile-001.png _images/isonitrile-002.png _images/isonitrile-003.png

isothiocyanate

_images/isothiocyanate-001.png _images/isothiocyanate-002.png _images/isothiocyanate-003.png

ketal

_images/ketal-001.png _images/ketal-002.png _images/ketal-003.png

ketone

_images/ketone-001.png _images/ketone-002.png _images/ketone-003.png

lactam

_images/lactam-001.png _images/lactam-002.png _images/lactam-003.png

lactone

_images/lactone-001.png _images/lactone-002.png _images/lactone-003.png

lawesson_s_reagent

_images/lawesson_s_reagent-001.png _images/lawesson_s_reagent-002.png _images/lawesson_s_reagent-003.png

malonic

_images/malonic-001.png _images/malonic-002.png _images/malonic-003.png

methoxyethoxymethyl_MEM

_images/methoxyethoxymethyl_MEM-001.png _images/methoxyethoxymethyl_MEM-002.png _images/methoxyethoxymethyl_MEM-003.png

methyl_ketone

_images/methyl_ketone-001.png _images/methyl_ketone-002.png _images/methyl_ketone-003.png

michael_acceptor

_images/michael_acceptor-001.png _images/michael_acceptor-002.png _images/michael_acceptor-003.png

monensin_derivatives

_images/monensin_derivatives-001.png _images/monensin_derivatives-002.png _images/monensin_derivatives-003.png

nitrile

_images/nitrile-001.png _images/nitrile-002.png _images/nitrile-003.png

nitro

_images/nitro-001.png _images/nitro-002.png _images/nitro-003.png

nitroso

_images/nitroso-001.png _images/nitroso-002.png _images/nitroso-003.png

N_methoyl

_images/N_methoyl-001.png _images/N_methoyl-002.png _images/N_methoyl-003.png

nonacylhydrazone

_images/nonacylhydrazone-001.png _images/nonacylhydrazone-002.png _images/nonacylhydrazone-003.png

noxide

_images/noxide-001.png _images/noxide-002.png _images/noxide-003.png

N_P_S_Halides

_images/N_P_S_Halides-001.png _images/N_P_S_Halides-002.png _images/N_P_S_Halides-003.png

NS_beta_halothyl

_images/NS_beta_halothyl-001.png _images/NS_beta_halothyl-002.png _images/NS_beta_halothyl-003.png

organometallic

_images/organometallic-001.png _images/organometallic-002.png _images/organometallic-003.png

oxalyl

_images/oxalyl-001.png _images/oxalyl-002.png _images/oxalyl-003.png

oxaziridine

_images/oxaziridine-001.png _images/oxaziridine-002.png _images/oxaziridine-003.png

oxime

_images/oxime-001.png _images/oxime-002.png _images/oxime-003.png

oxygen_cation

_images/oxygen_cation-001.png _images/oxygen_cation-002.png _images/oxygen_cation-003.png

paranitrophenyl_esters

_images/paranitrophenyl_esters-001.png _images/paranitrophenyl_esters-002.png _images/paranitrophenyl_esters-003.png

pentafluorophenyl_esters

_images/pentafluorophenyl_esters-001.png _images/pentafluorophenyl_esters-002.png _images/pentafluorophenyl_esters-003.png

perhalo_ketone

_images/perhalo_ketone-001.png _images/perhalo_ketone-002.png _images/perhalo_ketone-003.png

peroxide

_images/peroxide-001.png _images/peroxide-002.png _images/peroxide-003.png

phenol

_images/phenol-001.png _images/phenol-002.png _images/phenol-003.png

phosphanes

_images/phosphanes-001.png _images/phosphanes-002.png _images/phosphanes-003.png

phosphinic_acid

_images/phosphinic_acid-001.png _images/phosphinic_acid-002.png _images/phosphinic_acid-003.png

phosphonamide

_images/phosphonamide-001.png _images/phosphonamide-002.png _images/phosphonamide-003.png

phosphonic_acid

_images/phosphonic_acid-001.png _images/phosphonic_acid-002.png _images/phosphonic_acid-003.png

phosphonic_ester

_images/phosphonic_ester-001.png _images/phosphonic_ester-002.png _images/phosphonic_ester-003.png

phosphonylnitrile

_images/phosphonylnitrile-001.png _images/phosphonylnitrile-002.png _images/phosphonylnitrile-003.png

phosphoramides

_images/phosphoramides-001.png _images/phosphoramides-002.png _images/phosphoramides-003.png

phosphoranes

_images/phosphoranes-001.png _images/phosphoranes-002.png _images/phosphoranes-003.png

phosphoric_acid

_images/phosphoric_acid-001.png _images/phosphoric_acid-002.png _images/phosphoric_acid-003.png

phosphoric_ester

_images/phosphoric_ester-001.png _images/phosphoric_ester-002.png _images/phosphoric_ester-003.png

phosphoryl

_images/phosphoryl-001.png _images/phosphoryl-002.png _images/phosphoryl-003.png

phosphoryl

_images/phosphoryl-001.png _images/phosphoryl-002.png _images/phosphoryl-003.png

phthalimides_PHT

_images/phthalimides_PHT-001.png _images/phthalimides_PHT-002.png _images/phthalimides_PHT-003.png

polyenes

_images/polyenes-001.png _images/polyenes-002.png _images/polyenes-003.png

primary_amine

_images/primary_amine-001.png _images/primary_amine-002.png _images/primary_amine-003.png

propiolactones

_images/propiolactones-001.png _images/propiolactones-002.png _images/propiolactones-003.png

quinone

_images/quinone-001.png _images/quinone-002.png _images/quinone-003.png

saponin_derivatives

_images/saponin_derivatives-001.png _images/saponin_derivatives-002.png _images/saponin_derivatives-003.png

SCN2

_images/SCN2-001.png _images/SCN2-002.png _images/SCN2-003.png

secondary_amine

_images/secondary_amine-001.png _images/secondary_amine-002.png _images/secondary_amine-003.png

squalestatin_derivatives

_images/squalestatin_derivatives-001.png _images/squalestatin_derivatives-002.png _images/squalestatin_derivatives-003.png

sulfide

_images/sulfide-001.png _images/sulfide-002.png _images/sulfide-003.png

sulfinimine

_images/sulfinimine-001.png _images/sulfinimine-002.png _images/sulfinimine-003.png

sulfinylthio

_images/sulfinylthio-001.png _images/sulfinylthio-002.png _images/sulfinylthio-003.png

sulfonamide

_images/sulfonamide-001.png _images/sulfonamide-002.png _images/sulfonamide-003.png

sulfone

_images/sulfone-001.png _images/sulfone-002.png _images/sulfone-003.png

sulfonic_acid

_images/sulfonic_acid-001.png _images/sulfonic_acid-002.png _images/sulfonic_acid-003.png

sulfonic_ester

_images/sulfonic_ester-001.png _images/sulfonic_ester-002.png _images/sulfonic_ester-003.png

sulfonimine

_images/sulfonimine-001.png _images/sulfonimine-002.png _images/sulfonimine-003.png

sulfonyl_halide

_images/sulfonyl_halide-001.png _images/sulfonyl_halide-002.png _images/sulfonyl_halide-003.png

sulfonylnitrile

_images/sulfonylnitrile-001.png _images/sulfonylnitrile-002.png _images/sulfonylnitrile-003.png

sulfonylurea

_images/sulfonylurea-001.png _images/sulfonylurea-002.png _images/sulfonylurea-003.png

sulfoxide

_images/sulfoxide-001.png _images/sulfoxide-002.png _images/sulfoxide-003.png

t_butyl_ether

_images/t_butyl_ether-001.png _images/t_butyl_ether-002.png _images/t_butyl_ether-003.png

terminal_vinyl

_images/terminal_vinyl-001.png _images/terminal_vinyl-002.png _images/terminal_vinyl-003.png

tertiary_amine

_images/tertiary_amine-001.png _images/tertiary_amine-002.png _images/tertiary_amine-003.png

tetrahydropyran_THP

_images/tetrahydropyran_THP-001.png _images/tetrahydropyran_THP-002.png _images/tetrahydropyran_THP-003.png

thioamide

_images/thioamide-001.png _images/thioamide-002.png _images/thioamide-003.png

thiocarbamate

_images/thiocarbamate-001.png _images/thiocarbamate-002.png _images/thiocarbamate-003.png

thioester

_images/thioester-001.png _images/thioester-002.png _images/thioester-003.png

thiourea

_images/thiourea-001.png _images/thiourea-002.png _images/thiourea-003.png

triazine

_images/triazine-001.png _images/triazine-002.png _images/triazine-003.png

tricarbo_phosphene

_images/tricarbo_phosphene-001.png _images/tricarbo_phosphene-002.png _images/tricarbo_phosphene-003.png

trimethylsilyl_TMS

_images/trimethylsilyl_TMS-001.png _images/trimethylsilyl_TMS-002.png _images/trimethylsilyl_TMS-003.png

urea

_images/urea-001.png _images/urea-002.png _images/urea-003.png

New Rules

New rules specify additional functional groups or substructures that may be used. They must specify a substructure definition in the form of a SMARTS in addition to the substructure name and maximum limit. For example:

NEWRULE norbornane 1 C1CC2CCC1C2

The first field is the NEWRULE keyword. The second field defines the name associated with the substructure (primarily for logging purposes). The third field indicates the maximum number of the substructure that can be allowed. The fourth field is the SMARTS string for the substructure, norbornane in this case. This example rule would indicate that molecules with a single norbornane substructure would be allowable, but that those with 2 or more norbornanes would be eliminated.

New rules that have a name that is identical with one of the original rules take precedence over the original rule.

Selection Statements

The select statement allows a filter file to specify the required number of substructures in order to be able to pass the filter. These statements are similar to new rules except that they list a required range for passing the filter rather than the range for failing to pass the filter. For example:

SELECT amine 1 1 [N;!$(*-*[!#6;!#1]);!$(*-a);!$(*=,#*)]

The first field is the SELECT keyword. The second field indicates the name for the selection (again for logging purposes). The third field is the minimum number of substructures required to be in the molecule. The fourth field is the maximum number of substructures allowed in the molecule. The fifth field is the substructure defined by a SMARTS pattern. The example requires that molecules contain exactly one amine. Currently, only a single SELECT statement is allowed in the filter file. Any complex boolean substructure statements can be incorporated directly into the SMARTS. If multiple SELECT statements occur in a filter file, only the final one will be applied.

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